RetrogeneDB ID: retro_ogar_237

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873910.1:129794..131189(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000032031
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DCAF12
• Ensembl ID: ENSOGAG00000015799
• Aliases: None
• Description: DDB1 and CUL4 associated factor 12 [Source:HGNC Symbol;Acc:19911]

Sequence

>retro_ogar_237
TTGGCCCCGCAGCAAACAGGTAGCAGGAAGCGGAAAGCCCCCTCGGTTGAAGCGGGCGCTGGGAGCTCGTCGTCGCGGGG
GGCGGAGGCGGCGGTGGACGGAGAGGGACCAATGCTGCCCAAGAAGCAGAAGAGGCCAGCGAAGCGTCGCTCCCTGGCAC
ACTACCTGAGGGGCCGAGAGGTGGGCGCGCGGGGCCGCGCGGGGCTCCTGGGCTTCGAGGGCGAGCTGCGCGGGTACGCG
GTGCGGAGACTGCCAGAGCTGCTGACCGAGCGCCAGTTGGCCCTGGGCACCCTCAACAAGGTGTTCGCATCGCAGTGGCT
GAACACCAGACAGGTGGTGTGCGGCACCAAGTGTAACACGCTTTTCGTCGTGGACGTGCAGTCTGGCCACATCACACGCA
TTCCCCTTATGCAGGACAGGGTGCCTGGACTGGGCCGGGCCCAGCCAGGCTGTGGCATCCACGCCATTGAGCTGAATCCC
TCCAAGACGCTATTGGCCACCGGGGGTGAAAATCCAAACAGCTTGGCTATCTATCAGCTTCCCACCTTGGACCCCGTGTG
CCTGGGTGACCGCCACGGCCACAAGGACTGGATCTTTGCTGTCGCCTGGCTGAGTGACACAGTGGCTGTGAGTGGCTCCC
GAGACGGCACCGTGGCGCTGTGGAGATTGGACCCGGACATGTTCGATGGCAGCATTGCCTGGCACAAGGATGTGGGGCTC
CCTGTGTATGTCCACATCCGACCGAGGGATGTGGAGGCTATCCCCAGGGCCAGCACCAACTCCAGTAACCGCAAAGTGCG
AGCCCTGGCCTTCAGTGGCAAGAACCAGGAGCTGGGAGCAGTGTCCCTGGATGGCTACTTCCACCTGTGGAAAGCCCGGA
GCACTCTTTCCAGGTTACTGTCCATCAGGCTGCCCTACTGCCGAGAGAATGTGTGCCTAACCTACTGTGATGAGTTGTCC
CTGTACGCAGTAGGCTCCCAGTCCCATGTTTCTTTCCTGGATCCCCGTCAGCGCCAGCAGAATATCCGGCCTCTCTGTTC
CCGTGAGGGTGGCACAGGAGTGCGCTCCCTGAGCTTCTACCAGCACATCATCACTGTGGGCACGGGCCATGGCTCACTGC
TCTTCTATGACATCCGTGCCCATAAGTTCCTGGAGGAGAGGGCCTTGGCCAGCCCAGGCTCCTCTCCAGGGTCTTCAGGG
AGGAAGCTCAAGCTCACTTGTGGCAGAGGCTGGCTCAACCAGGATGACCTCTGGGTGAACTACTTTGGGGGCATTGGAGA
GTTTCCCAATGCGCTCTACACCCACTGCTACAACTGGCCTGAAATGAAGCTCTTTGTGGCCGGAGGTCCTCTCCCTTCAG
GCCTCCATGGAAATTATGCAGGCCTGTGGAGCTAA

Alignment

ORF - retro_ogar_237 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.8 %
• Parental protein coverage: 99.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARKAVSRKRKAPASPGAGSDAQDPQFGWDHSLHKRKRLPPVKRSLVYYLKNREVRLQNETN---YSRVLH
          .RK.......A.A.......A.....G....L.K....P...RSL..YL..REV..............L.
Retrocopy SRKRKAPSVEAGAGSSSSRGAEAAVDGEGPMLPKKQKRPAKRRSLAHYLRGREVGARGRAGLLGFEGELR

Parental  GYAAQQLPSLLKEREFHLGTLNKVFASQWLNHRQVVCGTKCNTLFVVDVQTSQITKIPILKDREPG-GVT
          GYA...LP.LL.ER...LGTLNKVFASQWLN.RQVVCGTKCNTLFVVDVQ...IT.IP...DR.PG.G..
Retrocopy GYAVRRLPELLTERQLALGTLNKVFASQWLNTRQVVCGTKCNTLFVVDVQSGHITRIPLMQDRVPGLGRA

Parental  QQGCGIHAIELNPSRTLLATGGDNPNSLAIYRLPTLDPVCVGD-DGHKDWIFSIAWISDTMAVSGSRDGS
          Q.GCGIHAIELNPS.TLLATGG.NPNSLAIY.LPTLDPVC.GD..GHKDWIF..AW.SDT.AVSGSRDG.
Retrocopy QPGCGIHAIELNPSKTLLATGGENPNSLAIYQLPTLDPVCLGDRHGHKDWIFAVAWLSDTVAVSGSRDGT

Parental  MGLWEVTDDVLTKSDARHNVSRVPVYAHITHKALKDIPKEDTNPDNCKVRALAFNNKNKELGAVSLDGYF
          ..LW....D....S.A.H.....PVY.HI.......IP...TN..N.KVRALAF..KN.ELGAVSLDGYF
Retrocopy VALWRLDPDMFDGSIAWHKDVGLPVYVHIRPRDVEAIPRASTNSSNRKVRALAFSGKNQELGAVSLDGYF

Parental  HLWKAENTLSKLLSTKLPYCRENVCLAYGSEWSVYAVGSQAHVSFLDPRQPSYNIKSVCSRERGSGIRSV
          HLWKA..TLS.LLS..LPYCRENVCL.Y..E.S.YAVGSQ.HVSFLDPRQ...NI...CSRE.G.G.RS.
Retrocopy HLWKARSTLSRLLSIRLPYCRENVCLTYCDELSLYAVGSQSHVSFLDPRQRQQNIRPLCSREGGTGVRSL

Parental  SFYEHIITVGTGQGSLLFYDIRAQRFLEERLSACYGAKPRLAGENLKLTTGKGWLNHDETWRNYFSDIDF
          SFY.HIITVGTG.GSLLFYDIRA..FLEER..A..G..P...G..LKLT.G.GWLN.D..W.NYF..I..
Retrocopy SFYQHIITVGTGHGSLLFYDIRAHKFLEERALASPGSSPGSSGRKLKLTCGRGWLNQDDLWVNYFGGIGE

Parental  FPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNYAGLWS
          FPNA.YTHCY.....KLFVAGGPLPSGLHGNYAGLWS
Retrocopy FPNALYTHCYNWPEMKLFVAGGPLPSGLHGNYAGLWS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_237 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000309	1 retrocopy	retro_amel_73,
Bos taurus	ENSBTAG00000021573	3 retrocopies	retro_btau_1794, retro_btau_1795, retro_btau_1796,
Equus caballus	ENSECAG00000023064	2 retrocopies	retro_ecab_1128, retro_ecab_1129,
Erinaceus europaeus	ENSEEUG00000013279	1 retrocopy	retro_eeur_403,
Microcebus murinus	ENSMICG00000005881	1 retrocopy	retro_mmur_14,
Macaca mulatta	ENSMMUG00000017458	1 retrocopy	retro_mmul_202,
Nomascus leucogenys	ENSNLEG00000004996	1 retrocopy	retro_nleu_6,
Otolemur garnettii	ENSOGAG00000015799	1 retrocopy	retro_ogar_237 ,
Ochotona princeps	ENSOPRG00000001281	2 retrocopies	retro_opri_1178, retro_opri_470,
Pongo abelii	ENSPPYG00000019127	1 retrocopy	retro_pabe_64,
Pteropus vampyrus	ENSPVAG00000008654	1 retrocopy	retro_pvam_16,
Sus scrofa	ENSSSCG00000010986	1 retrocopy	retro_sscr_17,
Ictidomys tridecemlineatus	ENSSTOG00000006904	1 retrocopy	retro_itri_168,
Tarsius syrichta	ENSTSYG00000014394	1 retrocopy	retro_tsyr_1965,
Tursiops truncatus	ENSTTRG00000010591	1 retrocopy	retro_ttru_8,